Ah yes the orange CHARGED Flecks grant 0.1 seconds to your timer when destroyed, so that's why the timer start increasing at some point. The purple OVERCHARGED Flecks explode when destroyed dealing damage to surrounding Flecks and allowing for a cascading effect. Both are briefly explained in the How To Play section on the main menu or pause menu. I'd hoped to better explain them in the upgrade tree at the point of first unlocking them, but ran out of time whilst desperately trying (and failing) to fix the OOM issue on the WEB build.
As for the bat, he was the first enemy you encounter, so his purpose was simply to be a distraction and get in the way, nothing more than that and can be ignored if you dot get annoying be him!
Hope that explains some of the points of confusion. Thanks so much for taking the time to play, and leave detailed feedback!